I had to reboot my BES server and after it came back up all of my users were assigned the "default" IT policy. The problem is that I had assigned them different IT policies before the reboot. Why would all users revert back to the default IT policy after I restarted the BES server?

Did something happen to your database? These settings are stored is the BES Configuration Database ... restarting the BES software wouldn't impact this. Perhaps check your ALRT and POLC logs around the time that you made this change and comment on anything that indicates an error / problem.